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Protocols

SchistoDB specifications

Information


Unique identifier OMICS_03137
Name SchistoDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Guilherme Oliveira

Publications for SchistoDB

SchistoDB citations

 (27)
library_books

Dynamic transcriptomes identify biogenic amines and insect like hormonal regulation for mediating reproduction in Schistosoma japonicum

2017
Nat Commun
PMCID: 5355954
PMID: 28287085
DOI: 10.1038/ncomms14693

[…] cripts ⩽150 bp in length were discarded. These three transcriptomes were merged to remove redundant sequences with blastn. S. japonicum expression databases (V4.0 and EST) were downloaded from http://schistoDB.net/. Finally, de novo reconstructed unigenes were annotated by blastx to public databases (the Swiss-Prot protein database, Caenorhabditis elegans transcriptome, Clonorchis sinensis transcr […]

call_split

Evidence for Integrin – Venus Kinase Receptor 1 Alliance in the Ovary of Schistosoma mansoni Females Controlling Cell Survival

2017
PLoS Pathog
PMCID: 5289644
PMID: 28114363
DOI: 10.1371/journal.ppat.1006147
call_split See protocol

[…] The following public domain tools were used: BLASTx (http://www.ncbi.nlm.nih.gov/BLAST), SchistoDB (http://schistodb.net/schisto/; []), and WormBase ParaSite (release 6, April 2016; http://parasite.wormbase.org/; []). The online-tool SMART (http://smart.embl-heidelberg.de/) [] was used to […]

library_books

Biompha LAMP: A New Rapid Loop Mediated Isothermal Amplification Assay for Detecting Schistosoma mansoni in Biomphalaria glabrata Snail Host

2016
PLoS Negl Trop Dis
PMCID: 5179122
PMID: 27941967
DOI: 10.1371/journal.pntd.0005225

[…] ther studies. Specificity for S. mansoni was tested in silico through BLAST alignment analysis [], as well as searches and comparisons in available online genomes databases for Schistosoma spp. (e.g. SchistoDB; http://schistodb.net/schisto/). A 284 bp unique region for S. mansoni was selected and used for LAMP primer design using the Primer Explorer v4 software (http://primerexplorer.jp/e/). A set […]

library_books

A Genome Wide Comparison to Identify Markers to Differentiate the Sex of Larval Stages of Schistosoma haematobium, Schistosoma bovis and their Respective Hybrids

2016
PLoS Negl Trop Dis
PMCID: 5115654
PMID: 27861520
DOI: 10.1371/journal.pntd.0005138

[…] atobium, S. bovis or to a chimeric concatenate of both genomes (allowing each read, depending on its origin, to map against the more similar location in one or the other species’ genome). We used the SchistoDB S. haematobium genome [] and the S. bovis draft assembly genome available at the Sanger institute website. The short alignment tool Bowtie2 [] was used; mapping was performed in single-end w […]

library_books

GPCR and IR genes in Schistosoma mansoni miracidia

2016
PMCID: 5080760
PMID: 27784323
DOI: 10.1186/s13071-016-1837-2

[…] The S. mansoni protein dataset used in this study was based on the improved genome assembly [], along with expression data provided by the GeneDB (www.genedb.org) and SchistoDB (www.schistodb.net) databases. To these databases, we applied Pfam-based profile searches and identification of TM domains with the goal of identifying receptors belonging to the rhodopsin G […]

library_books

Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment

2015
PLoS Negl Trop Dis
PMCID: 4492491
PMID: 26147973
DOI: 10.1371/journal.pntd.0003920

[…] mes, tBLASTn searches using each of the SmLy6 family members was performed against the latest publically available gene predictions (searches performed 17-08-2013) from those genomes (downloaded from SchistoDB.net and GeneDB.org respectively).Alignment of the SmLy6 family members and HsCD59 protein sequences was performed using MUSCLE software [] with additional manual editing based on canonical r […]

Citations

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SchistoDB institution(s)
Centro de Excelencia em Bioinformatica, National Institute for Science and Technology in Tropical Diseases FIOCRUZ-Minas, Belo Horizonte, Brazil; Laboratorio Multiusurio de Bioinformatica, Embrapa Informatica Agropecuaria, Campinas, Brazil; Shanghai Center for Bioinformation Technology, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Faculty of Veterinary Science, University of Melbourne, Parkville, VIC, Australia; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Biology, University of Pennsylvania, PA, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, GA, USA
SchistoDB funding source(s)
Supported by the National Institutes of Health (NIH) - Fogarty International Center [TW007012-03]; The Burroughs Wellcome Fund (BWF); CNPq [573839/2008-5]; FAPEMIG [CBB-1181/08485/2009, REDE-56/11] and EC FP7 [241865].

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